package gui.utils;

import core.rb.PB;
import core.rb.r.PR;
import java.util.HashMap;
import java.util.LinkedList;
import core.tree.Tree;

/*Author: John Archer, Contact: john.archer.jpa@gmail.com*/
public class Para{
    public static String EXTALNPATH = "";
    public static int PREDHPSMINM = 10;
    public static int PREDHPSPLUSM = 16;
    public static int PREDHPSLEN = 2;
    public static int PREDHPSMINMHIST = PREDHPSMINM;
    public static int PREDHPSPLUSMHIST = PREDHPSPLUSM;
    public static int PREDHPSLENHIST = PREDHPSLEN;
    public static double [][] POSTS = null;
    public static int POSTPROJID = -1;
    public static int TREEDAR_WIN = 50;
    public static Tree TDAR;
    public static int TREEDAR_MAG = 1000;
    public static int SPEED = 5;
    public static int BUFF = 0;
    public static String UNSORT = "";
    public static String BARCODES = "";
    public static int TOLERATE = 0;
    public static boolean DISPLAY_LEAF_NODES = true;
    public static boolean DISPLAY_LEAF_TITLES = false;
    public static String D_TITLE;
    public static String D_PATH;
    public static String P_TITLE;
    public static String PATH_TO_TEMPLATE;
    public static int TABLE_ROW = 0;
    public static Tree TREE;
    public static int TPOS = 0;
    public static int CTREE_MAG = Tree.INITIAL_TREE_MAG;
    public static int TREEWIN = 100;
    public static int TASK_TREEDAR = 5;
    public static int TASK_TREE = 6;
    public static int TASK_ADD_DATA = 10;
    public static int TASK_RM_DATA = 11;
    public static int TASK_DISPLAY = 13;
    public static int TASK_BARCODES = 16;
    public static int TASK_TSAVE = 17;
    public static int TASK_ADD_PROJ = 18;
    public static int TASK_RM_PROJ = 19;
    public static int TASK_FILTER = 21;
    public static int TASK_SAVE_FILTERED_TABLE = 22;
    public static int TASK_RSAVE = 23;
    public static int TASK_COUNT_STOP_CODONS = 24;
    public static int TASK_GENOTYPE = 25;
    public static int TASK_EXT_TREE = 26;
    public static int TASK_SAVE_INDELS = 27;
    public static int TASK_VEME = 28;
    public static int TASK_BATCH = 29;
    public static boolean UPDATEREF = false;
    public static HashMap <String, Integer> [] CODONS;
    public static int STOPS = 0;
    public static HeatMapData HEATMAP_DATA = null;
    public static int [] TREEDIDS;
    public static int PID = -1;
    public static int D_ID = -1;
    public static int P_ID_ADD_RM = -1;
    public static int D_ID_ADD_RM = -1;
    public static int [] HPS_CATS;
    public static PB PB;

    //reads to display
    public static LinkedList <PR> RTD = new LinkedList();
    public static int START_VERTICAL_VIEW;
    public static int END_VERTICAL_VIEW;
    public static int[][] NUCS;
    public static int INDEL_LEN_VIEW = 1;
    public static char [] CON;
    public static int NO_OF_ROWS = 16;
    public static int FRAME = 1;
    public static int[] TCODS = {-1, -1, -1, -1};

    public static boolean [] GENOCODS;
    public static boolean  [] GENOAA;
    public static String  GENOQUERY;
    
    public static String AAS[] = {"G", "E",  "D", "V", "A", "R", "S", "K", "N", "M", "I", "T", "W", "C", "Y", "F",  "Q", "H", "L", "P"};
    public static int KEYS_LEFT;
}